lib/SGN/Controller/Locus.pm

   1 package SGN::Controller::Locus;
   2
   3 =head1 NAME
   4
   5 SGN::Controller::Locus - Catalyst controller for the locus page
   6 (replacing the old cgi script)
   7
   8 =cut
   9
  10 use Moose;
  11 use namespace::autoclean;
  12
  13 use URI::FromHash 'uri';
  14
  15 use CXGN::Phenome::Locus;
  16 use CXGN::Phenome::Schema;
  17 use CXGN::Tools::Organism;
  18 use CXGN::Phenome::Locus::LinkageGroup;
  19
  20 BEGIN { extends 'Catalyst::Controller' }
  21 with 'Catalyst::Component::ApplicationAttribute';
  22
  23
  24 has 'schema' => (
  25     is       => 'rw',
  26     isa      => 'DBIx::Class::Schema',
  27     lazy_build => 1,
  28 );
  29
  30
  31
  32 sub locus_search : Path('/search/locus') Args(0) {
  33     my $self = shift;
  34     my $c = shift;
  35     my ($organism_names_ref, $organism_ids_ref)=CXGN::Tools::Organism::get_existing_organisms( $c->dbc->dbh);
  36
  37     unshift @$organism_names_ref, '';
  38     unshift @$organism_ids_ref, '';
  39     my @organism_ref;
  40     my $index;
  41     for my $id ( @$organism_ids_ref ) {
  42         push( @organism_ref, [$id, $organism_names_ref->[$index]] );
  43         $index++;
  44     }
  45     my $lg_names_ref =  CXGN::Phenome::Locus::LinkageGroup::get_all_lgs( $c->dbc->dbh );
  46     $c->stash(
  47         template       => '/search/loci.mas',
  48         organism_ref   => \@organism_ref,
  49         lg_names_ref   => $lg_names_ref,
  50         );
  51 }
  52
  53
  54
  55 sub _build_schema {
  56     shift->_app->dbic_schema( 'CXGN::Phenome::Schema' )
  57 }
  58
  59
  60 =head2 new_locus
  61
  62 Public path: /locus/0/new
  63
  64 Create a new locus.
  65
  66 Chained off of L</get_locus> below.
  67
  68 =cut
  69
  70 sub new_locus : Chained('get_locus') PathPart('new') Args(0) {
  71     my ( $self, $c ) = @_;
  72     $c->stash(
  73         template => '/locus/index.mas',
  74
  75         locusref => {
  76             action    => "new",
  77             locus_id  => 0 ,
  78             locus     => $c->stash->{locus},
  79             schema    => $self->schema,
  80         },
  81         );
  82 }
  83
  84
  85 sub view_by_name : Path('/locus/view/') Args(0) {
  86
  87     my ($self, $c) = @_;
  88
  89     my $symbol = $c->req->param("symbol");
  90     my $locusname  = $c->req->param("locus");
  91     my $species = $c->req->param("species");
  92
  93     my $locus_id = undef;
  94     my $locus = undef;
  95     if ($symbol && $species) {
  96         $locus = $c->stash->{locus} = CXGN::Phenome::Locus->new_with_symbol_and_species($c->dbc->dbh, $symbol, $species);
  97     }
  98
  99     if ($locusname) {
 100         $locus = $c->stash->{locus} = CXGN::Phenome::Locus->new_with_locusname($c->dbc->dbh, $locusname);
 101     }
 102
 103     if (defined($locus) && defined($locus->get_locus_id())) {
 104         $locus_id = $locus->get_locus_id();
 105         my $url = "/locus/$locus_id/view";
 106         $c->res->redirect($url, 301);
 107     }
 108     else {
 109         $c->stash->{template} = 'generic_message.mas';
 110         $c->stash->{message} = "No locus was found for the identifier provided ($symbol $locusname $species).";
 111         # forward to search page ?
 112     }
 113
 114
 115 }
 116
 117
 118 =head2 view_locus
 119
 120 Public path: /locus/<locus_id>/view
 121
 122 View a locus detail page.
 123
 124 Chained off of L</get_locus> below.
 125
 126 =cut
 127
 128 sub view_locus : Chained('get_locus') PathPart('view') Args(0) {
 129     my ( $self, $c, $action) = @_;
 130     my $locus = $c->stash->{locus};
 131     if( $locus ) {
 132         $c->forward('get_locus_extended_info');
 133     }
 134
 135     my $logged_user = $c->user;
 136     my $person_id   = $logged_user->get_object->get_sp_person_id if $logged_user;
 137     my $curator     = $logged_user->check_roles('curator') if $logged_user;
 138     my $submitter   = $logged_user->check_roles('submitter') if $logged_user;
 139     my $sequencer   = $logged_user->check_roles('sequencer') if $logged_user;
 140     my $dbh = $c->dbc->dbh;
 141
 142     my $trait_db_name => $c->get_conf('trait_ontology_db_name');
 143     ##################
 144
 145     ###Check if a locus page can be printed###
 146     my $locus_id = $locus ? $locus->get_locus_id : undef ;
 147
 148     print STDERR "LOCUS_ID: $locus_id ACTION: $action\n\n";
 149
 150     # print message if locus_id is not valid
 151     unless ( ( $locus_id =~ m /^\d+$/ ) || ($action eq 'new' && !$locus_id) ) {
 152         $c->throw_404( "No locus exists for that identifier." );
 153     }
 154     unless ( $locus || !$locus_id && $action && $action eq 'new' ) {
 155         $c->throw_404( "No locus exists for that identifier." );
 156     }
 157
 158     # print message if the locus is obsolete
 159     my $obsolete = $locus->get_obsolete();
 160     if ( $obsolete eq 't'  && !$curator ) {
 161         $c->throw(is_client_error => 0,
 162                   title             => 'Obsolete locus',
 163                   message           => "Locus $locus_id is obsolete!",
 164                   developer_message => 'only curators can see obsolete loci',
 165                   notify            => 0,   #< does not send an error email
 166             );
 167     }
 168
 169
 170     # print message if locus_id does not exist
 171     if ( !$locus && $action ne 'new' && $action ne 'store' ) {
 172         $c->throw_404('No locus exists for this identifier');
 173     }
 174
 175     ####################
 176     my $is_owner;
 177     my $owner_ids = $c->stash->{owner_ids} || [] ;
 178     if ( $locus && ($curator || $person_id && ( grep /^$person_id$/, @$owner_ids ) ) ) {
 179         $is_owner = 1;
 180     }
 181     my $dbxrefs = $self->locus_dbxrefs_by_db( $c );
 182     my $pubs = $self->_locus_pubs( $c);
 183     my $image_ids = $locus->get_figure_ids;
 184     my $cview_tmp_dir = $c->tempfiles_subdir('cview');
 185
 186     #########
 187     my @locus_xrefs =
 188         # 4. look up xrefs for all of them
 189         map $c->feature_xrefs( $_, { exclude => 'locuspages' } ),
 190         # 3. plus primary locus name
 191         $locus->get_locus_name,
 192         # 2. list of locus alias strings
 193         map $_->get_locus_alias,
 194         # 1. list of locus alias objects
 195         $locus->get_locus_aliases( 'f', 'f' );
 196     #########
 197     my ($feature, $src_feature) = $locus->get_src_feature;
 198 ################
 199     $c->stash(
 200         template => '/locus/index.mas',
 201         locusref => {
 202             action    => $action,
 203             locus_id  => $locus_id ,
 204             curator   => $curator,
 205             submitter => $submitter,
 206             sequencer => $sequencer,
 207             person_id => $person_id,
 208             user      => $logged_user,
 209             locus     => $locus,
 210             dbh       => $dbh,
 211             is_owner  => $is_owner,
 212             owners    => $owner_ids,
 213             dbxrefs   => $dbxrefs,
 214             pubs      => $pubs,
 215             cview_tmp_dir  => $cview_tmp_dir,
 216             cview_basepath => $c->get_conf('basepath'),
 217             image_ids      => $image_ids,
 218             xrefs      => \@locus_xrefs,
 219             trait_db_name => $trait_db_name,
 220             feature     => $feature,
 221             src_feature => $src_feature,
 222         },
 223         locus_add_uri  => $c->uri_for( '/ajax/locus/associate_locus' )->relative(),
 224         cvterm_add_uri => $c->uri_for( '/ajax/locus/associate_ontology')->relative(),
 225         assign_owner_uri  => $c->uri_for( '/ajax/locus/assign_owner' )->relative(),
 226         );
 227 }
 228
 229
 230 =head1 PRIVATE ACTIONS
 231
 232 =head2 get_locus
 233
 234 Chain root for fetching a locus object to operate on.
 235
 236 Path part: /locus/<locus_id>
 237
 238 =cut
 239
 240 sub get_locus : Chained('/')  PathPart('locus')  CaptureArgs(1) {
 241     my ($self, $c, $locus_id) = @_;
 242
 243     my $identifier_type = $c->stash->{identifier_type}
 244         || $locus_id =~ /[^-\d]/ ? 'locus' : 'locus_id';
 245
 246     if( $identifier_type eq 'locus_id' ) {
 247         if ( $locus_id == 0 ) {
 248             $c->stash->{locus}     = CXGN::Phenome::Locus->new($c->dbc->dbh);
 249             return 1;
 250         } elsif ( $locus_id < 0 ) {
 251             $c->throw_client_error( public_message => 'Locus ID must be a positive integer.' );
 252         }
 253     }
 254     #remove version numbers from locus name locus123.1.2
 255     while ( $locus_id =~ m/.*\.\d+/ ) {
 256         $locus_id =~ s/(.*)(\.\d+)/$1/ ;
 257     }
 258
 259     my $matching_loci = $self->schema->resultset('Locus')->search(
 260         {
 261             $identifier_type => $locus_id,
 262             obsolete         => 'f'
 263         } );
 264
 265     if( $matching_loci->count > 1 ) {
 266         $c->throw_client_error( public_message => 'Multiple matching loci' );
 267     }
 268
 269     my ( $locus ) = $matching_loci->all
 270         or $c->throw_404( "Locus not found" );
 271     my $found_locus_id = $locus->locus_id;
 272
 273     $c->stash->{locus}     = CXGN::Phenome::Locus->new($c->dbc->dbh, $found_locus_id);
 274
 275
 276     return 1;
 277 }
 278
 279
 280
 281
 282 sub get_locus_owner_ids : Private {
 283     my ( $self, $c ) = @_;
 284     my $locus = $c->stash->{locus};
 285     my @owner_ids = $locus ? $locus->get_owners : ();
 286     $c->stash->{owner_ids} = \@owner_ids;
 287 }
 288
 289 sub get_locus_owner_objects : Private {
 290     my ( $self, $c ) = @_;
 291     my $locus = $c->stash->{locus};
 292     my $owner_objects = $locus ? $locus->get_owners(1) : ();
 293     $c->stash->{owner_objects} = $owner_objects;
 294 }
 295
 296 sub get_locus_extended_info : Private {
 297     my ( $self, $c ) = @_;
 298     $c->forward('get_locus_owner_ids');
 299
 300
 301 }
 302
 303 #add the locus_dbxrefs to the stash.
 304 sub get_locus_dbxrefs : Private {
 305     my ( $self, $c ) = @_;
 306     my $locus = $c->stash->{locus};
 307     my $locus_dbxrefs = $locus->get_dbxrefs;
 308     $c->stash->{locus_dbxrefs} = $locus_dbxrefs;
 309 }
 310
 311 sub locus_dbxrefs_by_db : Private {
 312     my ( $self, $c ) = @_;
 313     my $locus = $c->stash->{locus};
 314     my %locus_dbxrefs = $locus->get_all_dbxrefs;
 315     $c->stash->{locus_dbxrefs_by_db} = \%locus_dbxrefs;
 316 }
 317
 318
 319 sub _locus_pubs : Private {
 320     my ($self, $c ) = @_;
 321     my  $dbxrefs  = $c->stash->{locus_dbxrefs_by_db};
 322
 323     my @sorted_pubs =  ${$dbxrefs}{PMID} ? sort { $a->[0]->get_accession() <=> $b->[0]->get_accession() } @{ ${$dbxrefs}{PMID} } : () ;
 324     my @sgn_ref =  ${$dbxrefs}{SGN_ref} ? @{ ${$dbxrefs}{SGN_ref} } : () ;
 325
 326     my @cxgn_pubs;
 327     my @pub_dbxrefs = ( @sorted_pubs, @sgn_ref );
 328     foreach my $d ( @pub_dbxrefs) {
 329         if ( $d->[1] eq '0') { #if the dbxref is not obsolete
 330             my $pub = CXGN::Chado::Publication->new( $c->dbc->dbh, $d->[0]->get_publication()->get_pub_id() );
 331             push @cxgn_pubs, $pub;
 332         }
 333     }
 334     $c->stash->{pubs} = \@cxgn_pubs;
 335 }
 336 __PACKAGE__->meta->make_immutable;